depristo 5a6892900e fixing oddities in duplicates ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@628 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-07 18:55:45 +00:00
..
fourbasecaller	Bring new command-line argument parsing system live.	2009-05-06 18:16:11 +00:00
gatk	fixing oddities in duplicates	2009-05-07 18:55:45 +00:00
illumina	Make output type identical to the bustard parser so the values can be easily swapped for one another.	2009-04-09 20:49:34 +00:00
indels	added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads)	2009-05-06 21:59:33 +00:00
samples	Added a sample xml marshaller / unmarshaller.	2009-04-07 22:28:16 +00:00
utils	For on and off-genotype primary bases, optionally compute the concordance of the secondary bases to their expected distributions. Each genotype has slightly different profiles.	2009-05-01 06:33:48 +00:00
ValidateSAM.java	generic declarations added here and there to eliminate a few annoying warnings; no consequential changes	2009-04-02 20:53:01 +00:00